Hi Mac, > I have noticed that going from refmac 5 (script) to generate fo-fc and > 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is not exactly the same electron density maps-I mean some differences are seen. > I have used the following columns in Coot (latest version): FOFCWT, > PHFOFCWT and 2FOFCWT, PH2FOFCWT. The .o map file was generated using FFT, MAPMASK and MAPMAN. > I want to know why I am not getting identical maps, and if there is a > solution to avoid this problem then I would really appreciate your help.
There could be any number of reasons; which is more likely would depend on the level of differences between the maps. In (rough) level of significance, the ones I can think of are: 1. inputs - are your scripts using the same columns as coot (if I'm understanding correctly that coot is calculating the maps on the fly for you)? 2. FFT specific stuff - are both maps being calculated using the same gridpoints and FFT algorithm? 3. contouring issues - the graphics programs may be using different contouring algorithms; if you're contouring by sigma/rms deviation, then this can be affected by the size of the region used for rms determination (are the maps the same size?). Map normalization may also be an issue. 4. Computational "noise" - I've been able to get non-identical maps just by changing the variable precision (identical input files) used by the programs. The differences are minimal, but observable. I'm assuming that you're using a single system for both maps, otherwise there could be additional issues (although these should also be relatively minor). One thing that shouldn't make a difference - O can directly read ccp4 formatted maps, so using FFT with xyzlim asu and reading in O with qmap or fmap should let you skip over the mapmask/mapman steps. As far as your specific case, run down the list of things that could have an effect (there may be other issues that I'm forgetting), and eventually you should find where the differences are. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
